chmiel_human_rnaseq

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        Note that additional data was saved in chmiel_human_rnaseq_multiqc_report_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.10.dev0

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        chmiel_human_rnaseq

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2022-03-08, 18:04 based on data in:

        Welcome! Not sure where to start?   Watch a tutorial video   (6:06)

        General Statistics

        Showing 12/12 rows and 2/2 columns.
        Sample Name% AlignedM Aligned
        ZEKI0001
        91.5%
        15.6
        ZEKI0002
        91.7%
        12.2
        ZEKI0003
        91.2%
        17.1
        ZEKI0004
        91.0%
        17.3
        ZEKI0005
        90.8%
        19.4
        ZEKI0006
        91.2%
        16.5
        ZEKI0007
        91.5%
        17.4
        ZEKI0008
        91.1%
        17.3
        ZEKI0009
        91.0%
        14.4
        ZEKI0010
        92.7%
        19.9
        ZEKI0011
        90.7%
        14.2
        ZEKI0012
        90.3%
        13.3

        STAR

        STAR is an ultrafast universal RNA-seq aligner.

        Alignment Scores

        Created with Highcharts 5.0.6# ReadsChart context menuExport PlotSTAR: Alignment ScoresUniquely mappedMapped to multiple lociMapped to too many lociUnmapped: too shortUnmapped: otherZEKI0001ZEKI0002ZEKI0003ZEKI0004ZEKI0005ZEKI0006ZEKI0007ZEKI0008ZEKI0009ZEKI0010ZEKI0011ZEKI001201M2M3M4M5M6M7M8M9M10M11M12M13M14M15M16M17M18M19M20M21M22M23MCreated with MultiQC

        Gene Counts

        Statistics from results generated using --quantMode GeneCounts. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.

           
        Created with Highcharts 5.0.6# ReadsChart context menuExport PlotSTAR: Gene CountsOverlapping GenesNo FeatureAmbiguous FeaturesMultimappingUnmappedZEKI0001ZEKI0002ZEKI0003ZEKI0004ZEKI0005ZEKI0006ZEKI0007ZEKI0008ZEKI0009ZEKI0010ZEKI0011ZEKI001201M2M3M4M5M6M7M8M9M10M11M12M13M14M15M16M17M18M19M20M21M22M23MCreated with MultiQC

        HTStream

        HTStream quality control and processing pipeline for High Throughput Sequencing data.

        Processing Overview

        General statistics from the HTStream pipeline.


        Preprocessing Statistics

        Created with Highcharts 5.0.6ToolValueChart context menuExport PlotHTStream: Preprocessing Statisticshts_Stats_1:GC_Contenthts_Stats_1: GC_Contenthts_Stats_1:N_Content x10^4hts_Stats_1: N_Content x 10^4hts_Stats_1:Q30_Fractionhts_Stats_1: Q30_Fractionhts_SeqScre…hts_SeqScreener_2: Percent_Hits x 10^1hts_SuperDe…hts_SuperDeduper_1: Percent_Duplicateshts_SuperDe…hts_SuperDeduper_1: Percent_Ignored x 10^4hts_Adapter…hts_AdapterTrimmer_1: Fraction_Bp_Losthts_Adapter…hts_AdapterTrimmer_1: Fraction_PE_Bp_Trimmedhts_Adapter…hts_AdapterTrimmer_1: Fraction_PE_Read_Trimmedhts_QWindo…hts_QWindowTrim_1: Fraction_R1_Bp_Trimmed_Left x 10^4hts_QWindo…hts_QWindowTrim_1: Fraction_R1_Bp_Trimmed_Right x 10^2hts_QWindo…hts_QWindowTrim_1: Fraction_R2_Bp_Trimmed_Left x 10^3hts_QWindo…hts_QWindowTrim_1: Fraction_R2_Bp_Trimmed_Right x 10^2hts_PolyATT…hts_PolyATTrim_1: Fraction_Bp_Lost x 10^3hts_NTrimm…hts_NTrimmer_1: Fraction_Bp_Lost x 10^4hts_LengthFi…hts_LengthFilter_1: Fraction_Reads_Lost x 10^2hts_Stats_2:GC_Contenthts_Stats_2: GC_Contenthts_Stats_2:Q30_Fractionhts_Stats_2: Q30_Fraction00.20.40.60.81Created with MultiQC

        Fragment Reduction

        Provides scaled statistics collected throughout the preprocessing pipeline, highlighting variable statistics across experiment.

        Created with Highcharts 5.0.6ToolCountsChart context menuExport PlotHTStream: Fragment ReductionPipeline Inputhts_Stats_1hts_SeqScreener_1hts_SeqScreener_2hts_SuperDeduper_1hts_LengthFilter_1hts_Stats_210000000125000001500000017500000200000002250000025000000275000003000000032500000Created with MultiQC

        Basepair Reduction

        Provides scaled statistics collected throughout the preprocessing pipeline, highlighting variable statistics across experiment.

        Created with Highcharts 5.0.6ToolCountsChart context menuExport PlotHTStream: Basepair ReductionPipeline Inputhts_Stats_1hts_AdapterTrimmer_1hts_QWindowTrim_1hts_PolyATTrim_1hts_NTrimmer_1hts_Stats_2300000000040000000005000000000600000000070000000008000000000900000000010000000000Created with MultiQC

        hts_Stats

        Generates a JSON formatted file containing a set of statistical measures about the input read data.

        Showing 12/12 rows and 6/6 columns.
        Sample Name% PE% R1 Q30% R2 Q30GC ContentN ContentNotes
        ZEKI0001
        100.00%
        92.82%
        93.58%
        45.84%
        0.0020%
        initial stats
        ZEKI0002
        100.00%
        93.19%
        93.68%
        46.83%
        0.0020%
        initial stats
        ZEKI0003
        100.00%
        92.54%
        93.28%
        46.42%
        0.0020%
        initial stats
        ZEKI0004
        100.00%
        93.09%
        93.23%
        46.78%
        0.0020%
        initial stats
        ZEKI0005
        100.00%
        93.07%
        92.98%
        46.30%
        0.0021%
        initial stats
        ZEKI0006
        100.00%
        93.19%
        93.27%
        46.33%
        0.0021%
        initial stats
        ZEKI0007
        100.00%
        93.01%
        93.39%
        46.86%
        0.0021%
        initial stats
        ZEKI0008
        100.00%
        93.19%
        93.15%
        46.69%
        0.0021%
        initial stats
        ZEKI0009
        100.00%
        92.71%
        93.21%
        47.51%
        0.0018%
        initial stats
        ZEKI0010
        100.00%
        93.83%
        93.93%
        46.14%
        0.0021%
        initial stats
        ZEKI0011
        100.00%
        92.88%
        93.18%
        46.47%
        0.0020%
        initial stats
        ZEKI0012
        100.00%
        92.28%
        92.28%
        46.91%
        0.0020%
        initial stats

        Read Lengths: Paired End

        Distribution of read lengths for each sample.

        Notice: Each sample has a uniform read length distribution.
        Showing 12/12 rows and 2/2 columns.
        Sample NameR1 Read LengthsR2 Read Lengths
        ZEKI0001
        151
        151
        ZEKI0002
        151
        151
        ZEKI0003
        151
        151
        ZEKI0004
        151
        151
        ZEKI0005
        151
        151
        ZEKI0006
        151
        151
        ZEKI0007
        151
        151
        ZEKI0008
        151
        151
        ZEKI0009
        151
        151
        ZEKI0010
        151
        151
        ZEKI0011
        151
        151
        ZEKI0012
        151
        151

        Base by Cycle: Paired End

        Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

        Created with Highcharts 5.0.6CycleAvg. Difference from 25%Chart context menuExport PlotHTStream: Base by Cycle (PE)1611162126313641465156616671768186919610110611111612112613113614114615115616116617117618118619119620120621121622122623123624124625125626126627127628128629129630102.557.51012.515Created with MultiQC

        Quality by Cycle: Paired End

        Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

        Created with Highcharts 5.0.6CycleMean Q ScoreChart context menuExport PlotHTStream: Mean Quality by Cycle (PE)1611162126313641465156616671768186919610110611111612112613113614114615115616116617117618118619119620120621121622122623123624124625125626126627127628128629129630133.53434.53535.53636.537Created with MultiQC

        hts_SeqScreener

        A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.

        Notice: No hits in any sample.

        hts_SeqScreener 2

        A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.

        Showing 12/12 rows and 3/3 columns.
        Sample NamePE hits% PE HitsNotes
        ZEKI0001
        461718
        2.0041%
        count the number of rRNA reads
        ZEKI0002
        513050
        2.8639%
        count the number of rRNA reads
        ZEKI0003
        684027
        2.6317%
        count the number of rRNA reads
        ZEKI0004
        735292
        2.7065%
        count the number of rRNA reads
        ZEKI0005
        851865
        2.8336%
        count the number of rRNA reads
        ZEKI0006
        768117
        3.0535%
        count the number of rRNA reads
        ZEKI0007
        734308
        2.8445%
        count the number of rRNA reads
        ZEKI0008
        770198
        2.8899%
        count the number of rRNA reads
        ZEKI0009
        727821
        3.2198%
        count the number of rRNA reads
        ZEKI0010
        659214
        2.3050%
        count the number of rRNA reads
        ZEKI0011
        507109
        2.4175%
        count the number of rRNA reads
        ZEKI0012
        555590
        2.8266%
        count the number of rRNA reads

        hts_SuperDeduper

        A reference free duplicate read removal tool.

        Showing 12/12 rows and 3/3 columns.
        Sample Name% Duplicates% IgnoredNotes
        ZEKI0001
        25.67%
        0.01%
        remove dups
        ZEKI0002
        25.46%
        0.01%
        remove dups
        ZEKI0003
        27.33%
        0.01%
        remove dups
        ZEKI0004
        29.57%
        0.01%
        remove dups
        ZEKI0005
        28.56%
        0.01%
        remove dups
        ZEKI0006
        27.46%
        0.01%
        remove dups
        ZEKI0007
        25.98%
        0.01%
        remove dups
        ZEKI0008
        28.42%
        0.01%
        remove dups
        ZEKI0009
        29.36%
        0.01%
        remove dups
        ZEKI0010
        24.57%
        0.01%
        remove dups
        ZEKI0011
        25.23%
        0.01%
        remove dups
        ZEKI0012
        24.66%
        0.01%
        remove dups

        SuperDeduper: Duplicate Saturation

        Plots the number of duplicates against the number of unique reads per sample.

        Created with Highcharts 5.0.6Total ReadsUnique ReadsChart context menuExport PlotHTStream: Duplicate Saturation200000040000006000000800000010000000120000001400000016000000180000002000000022000000240000002600000028000000300000000500000010000000150000002000000025000000Created with MultiQC

        hts_AdapterTrimmer

        Trims adapters which are sequenced when the fragment insert length is shorter than the read length.

        Showing 12/12 rows and 4/4 columns.
        Sample Name% Bp Lost% AdaptersAvg. Bps TrimmedNotes
        ZEKI0001
        8.08%
        73.95%
        33.02
        trim adapters
        ZEKI0002
        9.66%
        82.02%
        35.58
        trim adapters
        ZEKI0003
        9.62%
        81.00%
        35.87
        trim adapters
        ZEKI0004
        10.25%
        84.49%
        36.65
        trim adapters
        ZEKI0005
        10.70%
        85.56%
        37.78
        trim adapters
        ZEKI0006
        11.14%
        87.67%
        38.37
        trim adapters
        ZEKI0007
        10.01%
        82.80%
        36.53
        trim adapters
        ZEKI0008
        10.23%
        84.23%
        36.69
        trim adapters
        ZEKI0009
        10.53%
        85.42%
        37.23
        trim adapters
        ZEKI0010
        8.50%
        76.91%
        33.36
        trim adapters
        ZEKI0011
        9.16%
        79.16%
        34.96
        trim adapters
        ZEKI0012
        10.34%
        84.21%
        37.08
        trim adapters

        AdapterTrimmer: Trimmed Basepairs Composition

        Composition of basepairs trimmed from the ends of paired end and single end reads.

        Created with Highcharts 5.0.6BasepairsChart context menuExport PlotHTStream: Trimmed Bp Composition BargraphRead 1Read 2ZEKI0001ZEKI0002ZEKI0003ZEKI0004ZEKI0005ZEKI0006ZEKI0007ZEKI0008ZEKI0009ZEKI0010ZEKI0011ZEKI0012025M50M75M100M125M150M175M200M225M250M275M300M325M350M375M400M425M450M475M500M525M550M575M600M625M650M675M700M725M7…750MCreated with MultiQC

        hts_QWindowTrim

        Uses a sliding window approach to remove the low quality ends of reads.

        Showing 12/12 rows and 5/5 columns.
        Sample Name% Bp Lost% R1 of Bp Lost% R2 of Bp LostAvg. Bps TrimmedNotes
        ZEKI0001
        0.22%
        47.21%
        52.79%
        0.61
        quality trim the ends of reads
        ZEKI0002
        0.21%
        48.74%
        51.26%
        0.58
        quality trim the ends of reads
        ZEKI0003
        0.27%
        41.46%
        58.54%
        0.74
        quality trim the ends of reads
        ZEKI0004
        0.26%
        39.90%
        60.10%
        0.71
        quality trim the ends of reads
        ZEKI0005
        0.26%
        40.47%
        59.53%
        0.71
        quality trim the ends of reads
        ZEKI0006
        0.24%
        42.57%
        57.43%
        0.65
        quality trim the ends of reads
        ZEKI0007
        0.25%
        35.87%
        64.13%
        0.68
        quality trim the ends of reads
        ZEKI0008
        0.24%
        41.27%
        58.73%
        0.65
        quality trim the ends of reads
        ZEKI0009
        0.28%
        38.13%
        61.87%
        0.75
        quality trim the ends of reads
        ZEKI0010
        0.18%
        41.20%
        58.80%
        0.51
        quality trim the ends of reads
        ZEKI0011
        0.28%
        39.14%
        60.86%
        0.78
        quality trim the ends of reads
        ZEKI0012
        0.30%
        38.16%
        61.84%
        0.81
        quality trim the ends of reads

        QWindowTrim: Trimmed Basepairs Composition

        Plots the number of low quality basepairs trimmed from ends of paired end and single end reads.

           
        Created with Highcharts 5.0.6BasepairsChart context menuExport PlotHTStream: QWindowTrim Trimmed Basepairs BargraphLeft TrimmmedRight TrimmmedZEKI0001ZEKI0002ZEKI0003ZEKI0004ZEKI0005ZEKI0006ZEKI0007ZEKI0008ZEKI0009ZEKI0010ZEKI0011ZEKI001205101520253035404550556065707580859095100Created with MultiQC

        hts_PolyATTrim

        Attempts to trim poly-A and poly-T sequences from the end of reads.

        Showing 12/12 rows and 5/5 columns.
        Sample Name% Bp Lost% R1 of Bp Lost% R2 of Bp LostAvg. Bps TrimmedNotes
        ZEKI0001
        0.07%
        61.07%
        38.93%
        0.20
        remove polyAT
        ZEKI0002
        0.07%
        61.87%
        38.13%
        0.18
        remove polyAT
        ZEKI0003
        0.08%
        62.69%
        37.31%
        0.21
        remove polyAT
        ZEKI0004
        0.07%
        61.48%
        38.52%
        0.20
        remove polyAT
        ZEKI0005
        0.08%
        62.26%
        37.74%
        0.21
        remove polyAT
        ZEKI0006
        0.07%
        58.35%
        41.65%
        0.19
        remove polyAT
        ZEKI0007
        0.07%
        60.10%
        39.90%
        0.18
        remove polyAT
        ZEKI0008
        0.07%
        60.14%
        39.86%
        0.19
        remove polyAT
        ZEKI0009
        0.07%
        63.47%
        36.53%
        0.19
        remove polyAT
        ZEKI0010
        0.06%
        56.82%
        43.18%
        0.17
        remove polyAT
        ZEKI0011
        0.07%
        60.66%
        39.34%
        0.20
        remove polyAT
        ZEKI0012
        0.07%
        58.63%
        41.37%
        0.19
        remove polyAT

        hts_NTrimmer

        Trims reads to the longest subsequence that contains no N's.

        Showing 12/12 rows and 5/5 columns.
        Sample NameTotal Bp Lost% R1 of Bp Lost% R2 of Bp Lost% DiscardedNotes
        ZEKI0001
        382222
        87.77%
        12.23%
        0.00%
        remove any remaining N bases
        ZEKI0002
        274804
        87.82%
        12.18%
        0.00%
        remove any remaining N bases
        ZEKI0003
        401067
        87.61%
        12.39%
        0.00%
        remove any remaining N bases
        ZEKI0004
        381633
        87.71%
        12.29%
        0.00%
        remove any remaining N bases
        ZEKI0005
        447675
        87.04%
        12.96%
        0.00%
        remove any remaining N bases
        ZEKI0006
        383837
        87.83%
        12.17%
        0.00%
        remove any remaining N bases
        ZEKI0007
        400141
        87.74%
        12.26%
        0.00%
        remove any remaining N bases
        ZEKI0008
        400764
        88.04%
        11.96%
        0.00%
        remove any remaining N bases
        ZEKI0009
        298800
        89.42%
        10.58%
        0.00%
        remove any remaining N bases
        ZEKI0010
        473563
        88.03%
        11.97%
        0.00%
        remove any remaining N bases
        ZEKI0011
        340289
        87.57%
        12.43%
        0.00%
        remove any remaining N bases
        ZEKI0012
        310238
        86.97%
        13.03%
        0.00%
        remove any remaining N bases

        NTrimmer: Trimmed Basepairs Composition

        Plots the number of N bases trimmed from ends of paired end and single end reads.

           
        Created with Highcharts 5.0.6BasepairsChart context menuExport PlotHTStream: NTrimmer Trimmed Basepairs BargraphLeft TrimmmedRight TrimmmedZEKI0001ZEKI0002ZEKI0003ZEKI0004ZEKI0005ZEKI0006ZEKI0007ZEKI0008ZEKI0009ZEKI0010ZEKI0011ZEKI001205101520253035404550556065707580859095100Created with MultiQC

        hts_LengthFilter

        Discards reads below a minimum length threshold.

        Showing 12/12 rows and 2/2 columns.
        Sample Name% PE LostNotes
        ZEKI0001
        0.28%
        remove reads < 50 bp
        ZEKI0002
        0.44%
        remove reads < 50 bp
        ZEKI0003
        0.52%
        remove reads < 50 bp
        ZEKI0004
        0.52%
        remove reads < 50 bp
        ZEKI0005
        0.67%
        remove reads < 50 bp
        ZEKI0006
        0.74%
        remove reads < 50 bp
        ZEKI0007
        0.54%
        remove reads < 50 bp
        ZEKI0008
        0.52%
        remove reads < 50 bp
        ZEKI0009
        0.62%
        remove reads < 50 bp
        ZEKI0010
        0.27%
        remove reads < 50 bp
        ZEKI0011
        0.48%
        remove reads < 50 bp
        ZEKI0012
        0.63%
        remove reads < 50 bp

        hts_Stats 2

        Generates a JSON formatted file containing a set of statistical measures about the input read data.

        Showing 12/12 rows and 6/6 columns.
        Sample Name% PE% R1 Q30% R2 Q30GC ContentN ContentNotes
        ZEKI0001
        100.00%
        97.35%
        97.18%
        44.22%
        0.0000%
        final stats
        ZEKI0002
        100.00%
        97.55%
        97.42%
        44.99%
        0.0000%
        final stats
        ZEKI0003
        100.00%
        97.36%
        97.12%
        44.35%
        0.0000%
        final stats
        ZEKI0004
        100.00%
        97.53%
        97.12%
        44.60%
        0.0000%
        final stats
        ZEKI0005
        100.00%
        97.49%
        96.99%
        44.59%
        0.0000%
        final stats
        ZEKI0006
        100.00%
        97.63%
        97.27%
        44.73%
        0.0000%
        final stats
        ZEKI0007
        100.00%
        97.56%
        97.07%
        44.98%
        0.0000%
        final stats
        ZEKI0008
        100.00%
        97.58%
        97.09%
        44.87%
        0.0000%
        final stats
        ZEKI0009
        100.00%
        97.59%
        96.99%
        45.20%
        0.0000%
        final stats
        ZEKI0010
        100.00%
        97.81%
        97.43%
        44.59%
        0.0000%
        final stats
        ZEKI0011
        100.00%
        97.41%
        96.95%
        44.82%
        0.0000%
        final stats
        ZEKI0012
        100.00%
        97.30%
        96.63%
        45.07%
        0.0000%
        final stats

        Read Lengths: Paired End

        Distribution of read lengths for each sample.


        Base by Cycle: Paired End

        Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

        Created with Highcharts 5.0.6CycleAvg. Difference from 25%Chart context menuExport PlotHTStream: Base by Cycle (PE)1611162126313641465156616671768186919610110611111612112613113614114615115616116617117618118619119620120621121622122623123624124625125626126627127628128629129630102.557.51012.515Created with MultiQC

        Quality by Cycle: Paired End

        Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

        Created with Highcharts 5.0.6CycleMean Q ScoreChart context menuExport PlotHTStream: Mean Quality by Cycle (PE)1611162126313641465156616671768186919610110611111612112613113614114615115616116617117618118619119620120621121622122623123624124625125626126627127628128629129630137.2537.537.753838.2538.538.753939.2539.5Created with MultiQC